I think it'd be better to navigate in a long thread if the layout is hierarchical like yahoo groups where comments can be expanded and collapsed. In sequential layout it's not easy to trace why one arrives at a certain comment, because we need to jump to several pages (more pages compared to hierarchical layout) just to find where he started commenting. Also it's hard to see the branching of comments.

That is the older style and in my opinion, the out-dated mode of forums. You only get to see the title unless you expand it, which doesn't tell you much about what is in the post. Most posts are short enough that this is not needed. I think over the years forum users have come to realize that it is better to keep posts, for the most part, short and simple. Long posts do not get read nearly as much as shorter ones. Call it psychology or whatever, but most people would rather read 20 short posts than one long one, even if there are more words in the 20 short posts (combined).